Elastic Behaviors of Adsorbed Protein-like Chains

Elastic behaviors of protein-like chains are investigated by Pruned-Enriched-Rosenbluth method and modified orientation-dependent monomer-monomer interactions model. The protein-like chain is pulled away from the attractive surface slowly with elastic force acting on it. Strong adsorption interaction and no adsorption interaction are both considered. We calculate the characteristic ratio and shape factor of protein-like chains in the process of elongation. The conformation change of the protein-like chain is well depicted. The shape of chain changes from “rod” to “sphere” at the beginning of elongation. Then, the shape changes from “sphere” to “rod”. In the end, the shape becomes a “sphere” as the chain leaves away from the surface. In the meantime, we discuss average Helmoholtz free energy per bond, average energy per bond, average adsorbed energy per bond, average α-helical energy per bond, average β-sheet energy per bond and average contact energy per bond.On the other hand, elastic force is also studied. It is found that elastic force has a long plateau during the tensile elongation when there exists adsorption interaction. This result is consistent with SMFS experiment of general polymers. Energy contribution to elastic force and contact energy contribution to elastic force are both discussed. These investigations can provide some insights into the elastic behaviors of adsorbed protein chains.     

Brownian dynamics simulations of polyelectrolyte adsorption onto topographically patterned surfaces

The effect of patterned surface topography on the adsorption of single polyelectrolyte molecules is explored using Brownian dynamics simulations. The polyelectrolyte is modeled as a free-draining, freely jointed bead-rod chain, and electrostatic interactions are incorporated using a screened Coulombic potential with excluded volume interactions accounted for by the repulsive part of a Lennard-Jones potential. Topography consisting of periodically spaced valleys of square cross section separated by flat hills is considered. Chain conformations are characterized for a wide range of valley widths, depths, and spacings as well as for several different types of surface charge distributions. Depending on the parameter values describing the topography, the chains are found to adopt conformations ranging from flat and extended to those associated with bridge-, brush-, or semi-bridge-like structures. The formation of these structures is rationalized on the basis of a free-energy model that takes into account the increase in free energy due to entropic confinement, excluded volume interactions, and chain stretching as well as the decrease in free energy due to bead-surface electrostatic attraction. The results of this work are expected to be useful in designing patterned surface topography to control the conformations of adsorbed polyelectrolyte molecules.     

Mesoscopic analysis of conformational and entropic contributions to nonspecific adsorption of HP copolymer chains using dynamic Monte Carlo simulations

Dynamic Monte Carlo simulations of short linear HP-type copolymers exhibiting proteinlike characteristics are used to investigate both chain dynamics and changes in chain conformational entropy and their contributions to the energetics of adsorption onto a solid-liquid interface. The dMC results show that the conformations and energies of adsorbed chains are highly degenerate. The ensemble-averaged energy of the adsorbed state is dependent on temperature, chain sequence, native-state stability, and sorbent surface geometry and hydrophobicity. Mesoscopic thermodynamic analyses reveal that, although increased chain conformational entropy contributes to the driving force for adsorption in certain cases, many conditions exist where the change in conformational entropy is either negligible or unfavorable due to constraints imposed by the need to form a large and specific number of favorable intra- and intermolecular contacts and by the impenetrable nature of the sorbent surface. Step-number-averaged energy trajectories, based on sampling of a large number of energy trajectories and thus conformational states at each step number, suggest that the search for a global energy minimum is gradual, so that adsorption is first reversible but becomes apparently irreversible with longer exposure to the sorbent. These results appear to be connected to the conformational adaptability of the chain both on the surface and in solution, and an adsorption model taking chain conformational dynamics into account is proposed.     

Energy landscapes for adsorption of a protein-like HP chain as a function of native-state stability

Dynamic Monte Carlo (DMC) simulations of the adsorption of simple protein-like chains are used to more clearly define the molecular basis for the dependence of adsorption thermodynamics on the stability of the unique lowest-energy "native state" conformation of the chain. Arai and Norde were among the first to show that proteins of low native-state stability strongly denature upon adsorption to weakly attractive sorbent surfaces, while relatively modest changes in conformation are observed in stable proteins under identical adsorption conditions. When the protein has a low native-state stability, favorable adsorption entropies are typically observed in such systems, leading to the general belief that the chain gains conformational entropy during adsorption through a net reduction in intramolecular interactions specific to the native-state structure. Analysis of energy landscapes generated from our DMC simulation results show that a net loss in specific intramolecular interactions can lead to a positive delta(ads)S under certain adsorption conditions. However, the influence of chain conformation on delta(ads)S is found to correlate more directly with the manner in which the unique states of the system are distributed among the energy levels available to the adsorbed chain. Delta(ads)S is found to tend toward a maximum for adsorption processes described by thermally averaged energy landscapes in which the energy levels carrying the highest Boltzmann weights have a high degree of conformational degeneracy. This condition is met when the average interaction energy between the chain and the sorbent equals that between two hydrophobic segments of the chain.     

sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections

An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near‐native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance‐scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar‐polar and polar‐nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main‐chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state‐of‐the‐art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM‐score). © 2016 Wiley Periodicals, Inc.     

Monte Carlo Calculations of Polymer Adsorption at the Entrance of Cylindrical Pores in Flat Adsorbing Surfaces

The influence of surface interactions on the conformation of flexible polymers partially confined inside narrow cylindrical pores in a flat surface is studied above the critical adsorption energy in a good solvent. We use a static configurational bias computational sampling method to calculate the adsorption free energy and the radius of gyration components parallel and perpendicular to the pore axis as a function of the polymer center of mass position at different degrees of confinement. We find strong free‐energy minima just in front of the pore entry for all degrees of confinement studied. At the location of the free‐energy minimum, polymers are partially adsorbed inside the pore and on the outer solid surface and adopt “drawing pin”‐like conformations. A distinct maximum in the average loop length at the pore entry indicates that the polymer bridges the pore entry of small pores.     

吸附类蛋白质分子二级结构变化的研究

采用蒙特卡罗方法和基于三维格点的ODI模型,研究了类蛋白质分子二级结构变化与表面吸附能的关系.分别计算了链长为29,39,49时、不同吸附能下类蛋白质分子二级结构的个数.包括α螺旋、β折叠、紧密接触对.吸附能参数aε<2εh时,这三类二级结构个数均没有明显的变化,而在2εh<εa<4εh,二级结构的个数迅速减小,εa>4hε时,二级结构的个数基本维持不变.同时发现吸附能增强对螺旋结构变化的影响最大,对折叠结构的影响其次,对紧密接触对影响最小.这体现在螺旋结构的减小幅度为90%,折叠结构减小的幅度为45%,而紧密接触对减小的幅度为35%.通过统计吸附单体个数,得到当吸附单体占总单体数的40%时,二级结构开始变化,直至吸附单体为总单体数的90%时,二级结构基本不变.另外还计算了二级结构个数的涨落δNh、δNc以及吸附单体个数的涨落δNa.在εa>2εh时,涨落突然增大,在aε=2εh时,δNh和δNb具有涨落极大值,这是二级结构相变的临界点.在εa=3.75εh处,δNc和δNa具有极大值.     

ELASTIC BEHAVIOR OF PROTEIN-LIKE SINGLE CHAIN

The conformational properties and elastic behaviors of protein-like single chains in the process of tensile elongation were investigated by means of Monte Carlo method. The sequences of protein-like single chains contain two types of residues: hydrophobic (H) and hydrophilic (P). The average conformations and thermodynamics statistical properties of protein-like single chains with various elongation ratio λ were calculated. It was found that the mean-square end-to-end distance r increases with elongation ratio,λ. The tensor eigenvalues ratio of : decreases with elongation ratio λ for short (HP)x protein-like polymers, however, the ratio of : increases with elongation ratioλ,especially for long (H)x sequence. Average energy per bond increases with elongation ratioλ, especially for(H)x protein-like single chains. Helmholtz free energy per bond also increases with elongation ratioλ. Elastic force (f), energy contribution to force (fU) and entropy contribution to force (fs) for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.     

ADSORPTION OF SHORT TWO-DIMENSIONAL COMPACT CHAINS

Short two-dimensional compact chains adsorbed on the attractive surface at different temperatures were investigated by using the enumeration calculation method. First we investigate the chain size and shape of adsorbed chains, such as characteristic ratios of mean-square radii of gyration 〈S^2〉x/N and 〈S^2〉y/N, shape factor 〈δ〉, and the orientation of chain bonds 〈cos^2 θ〉 to illuminate how the size and shape of adsorbed compact chains change with increasing temperatures. There are some special behaviors for the chain size and shape at low temperature, especially for strong attraction interaction. In the meantime, adsorbed compact chains have different behaviors from general adsorbed polymer chains. Some thermodynamics properties are also discussed here. Heat capacity changes non-monotonously, first increases and then reduces. The transition temperature Tc is nearly 1.0, 1.4, 2.0 and 4.2 （in the unit of To） for the case of ε = 0, -1, -2 and -4 （in the unit of kTo）, respectively. Average energy per bond increases while average Helmholtz free energy per bond decreases with increasing temperatures. From these two thermodynamics parameters we can also get another transition temperature Tc＇, and it is close to 0.7, 1.1, 1.5 and 3.4 for ε= 0, -1, -2, and -4, respectively. Therefore, Tc is greater than Tc＇ under the same condition. These investigations may provide some insights into the thermodynamics behaviors of adsorbed protein-like chains.     

Adsorption of interacting oligomers and polymers at an interface

We discuss in a qualitative way the physical background of a recently developed polymer adsorption theory, in which all the possible chain conformations for interacting chain molecules near an adsorbing interface are taken into account. Any conformation is described as a step-weighted random walk in a lattice. Each step is weighted according to a segmental weighting factor that contains the adsorption energy (for segments in contact with the surface), the entropy of mixing, and the attraction or repulsion between segments and solvent molecules. A suitable computing method is used to calculate the contribution of all chain conformations to the concentration profile, to the adsorbed amount, to the fraction of trains, loops and tails, to the layer thickness, etc. The theory is valid for any chain length and any concentration in the solution.Results for various chain lengths are given. Oligomers have a low affinity for the surface, whereas polymer adsorption isotherms are of the well known high affinity type. Three concentration regimes can be distinguished. In (extremely) dilute solutions the molecules on the surface adsorb as isolated chains (the Henry region).     

Adsorption of N-Decyl-N,N,N-trimethylammonium triflate (DeTATf), a cationic surfactant, on the Au(111) electrode surface

The adsorption behavior of the cationic surfactant N-decyl-N,N,N-trimethylammonium triflate (DeTATf) on the Au(111) electrode surface was characterized using cyclic voltammetry, differential capacity, and chronocoulometry. The thermodynamics of the ideally polarized electrode have been employed to determine the Gibbs excess and the Gibbs energy of adsorption. The results show that the adsorption of DeTATf has a multistate character. At low bulk DeTATf concentrations, the adsorption state is consistent with the formation of an adsorbed film of nearly flat molecules. At higher concentrations this film may represent a three-dimensional aggregated state. At negative potentials and charge densities close to 0 microC cm-2, the data suggest the formation of a film of tilted molecules oriented with the hydrocarbon tail toward the metal surface and the polar head toward the solution. A surprising result of this study is that DeTATf displays adsorption characteristics of a zwitterionic rather than a cationic surfactant. This behavior indicates that the adsorbed species is an ion pair.     

Conformational behavior of polymers adsorbed on nanotubes

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.     

Properties of Star-Branched Polymer Chains Near a Surface

We considered two model systems of star-branched polymers near an impenetrable surface. The model chains were constructed on a simple cubic lattice. Each star polymer consisted of f = 3 arms of equal length and the total number of segments was up to 799. The excluded volume effect was included into these models only and therefore the system was studied at good solvent conditions. In the first model system polymer chain was terminally attached with one arm to the surface. The grafted arm could slide along the surface. In the second system the star-branched chain was adsorbed on the surface and the strength of adsorption was were varied. The simulations were performed using the dynamic Monte Carlo method with local changes of chain conformations. The internal and local structures of a polymer layer were determined. The lateral diffusion and internal mobility of star-branched chains were studied as a function of strength of adsorption and the chain length. The lateral diffusion and internal mobility of star-branched chains were studied as a function of strength of adsorption and the chain length. It was shown that the behavior of grafted and weakly adsorbed chains was similar to that of a free three-dimensional polymer, while the strongly adsorbed chains behave as a two-dimensional system.     

Enhanced adsorption of arsenic onto maghemites nanoparticles: As(III) as a probe of the surface structure and heterogeneity

When normalized per unit of surface area, the quantity of arsenic adsorbed at the maghemite surface remains constant for particles between 300 and 20 nm. However, nanoparticles smaller than 20 nm exhibit enhanced adsorption capacity. The origin of this observed size-dependence for adsorption or "nano effect" is unclear. Arsenic was chosen as a probe of the surface structure to explore adsorption mechanisms occurring at the surface of maghemite nanoparticles (6 nm). Two factors contributing to the enhanced reactivity of nanoscale maghemites were determined. The first is related to a size-dependent structural modification of the surface of particles and the decrease of the occupancy of the tetrahedral site that leaves vacant, highly reactive adsorption sites. In particular, there is a site localized in a six-membered iron octahedral ring. This site is the only one for which an oxidation of As(III) occurs. The second factor relates to the thermodynamics of a decrease of the surface free energy. The high density of As adsorbed at the saturation of the surface can be related to crystal growth.     

Distribution and modification of sorption sites in amphiphilic calixarene-based solid lipid nanoparticles from hyperpolarized 129Xe NMR spectroscopy

The site distribution and accessibility in amphiphilic calixarenes-based solid lipid nanoparticles were determined as a function of lipid chain length using in situ 129Xe NMR spectroscopy with flowing hyperpolarized Xe gas. The study illustrates that host cavities in as-prepared materials are increasingly occluded by the lipid chain for compounds with chain lengths from C6 to C12 and are almost completely occluded for C14 and C16 chain lengths. Host cavities present at the surface of the particles are still accessible to small atoms (xenon) and organic molecules (methylene chloride, etc). The Xe spectra show that the accessible void space can be increased remarkably by exposure of the particle surface to suitably sized guest molecules that appear to displace the occluding hydrocarbon chains from the host cavities by competitive adsorption. This postsynthesis treatment thus modifies the state of self-assembly and improves sorption capability. The HP Xe NMR approach presented is suitable for small samples (a few milligrams) of SLNs, likely also for other biomaterials such as vesicles, model membranes, etc.     

Force microscopy studies of fibronectin adsorption and subsequent cellular adhesion to substrates with well-defined surface chemistries

Molecular force spectroscopy was used to study the mechanical behavior of plasma fibronectin (FN) on mica, gold, poly(ethylene glycol), and -CH(3), -OH, and -COOH terminated alkanethiol self-assembled monolayers. Proteins were examined at two concentrations, one resulting in a saturated surface with multiple intermolecular interactions referred to as the aggregate state and another resulting in a semiaggregate state where the proteins were neither completely isolated nor completely aggregated. Modeling of the force-extension data using two different theories resulted in similar trends for the fitted thermodynamic parameters from which insight into the protein's binding state could be obtained. Aggregated proteins adsorbed on hydrophobic surfaces adopted more rigid conformations apparently as a result of increased surface denaturation and tighter binding while looser conformations were observed on more hydrophilic surfaces. Studies of FN in a semiaggregate state showed heterogeneity in the model's thermodynamic parameters suggesting that, in the early stages of nonspecific adsorption, multiple protein conformations exist, each having bound irreversibly to the substrate. Proteins in this state all demonstrated a more rigid conformation than in the corresponding aggregate studies due to the greater number of substrate contacts available to the protein. Finally, the force spectroscopy experiments were examined for any biocompatibility correlation by seeding substrates with human umbilical vascular endothelial cells. As predicted from the models used in this work, surfaces with aggregated FN promoted cellular deposition while surfaces with FN in a semiaggregate state appeared to hinder cellular deposition and growth. The atomic force microscope's use as a means for projecting surface biocompatibility, although requiring additional testing, does look promising.     

Adsorption of atomic and molecular oxygen on the LaMnO3(001) surface: ab initio supercell calculations and thermodynamics

We present and discuss the results of ab initio DFT plane-wave supercell calculations of the atomic and molecular oxygen adsorption and diffusion on the LaMnO(3) (001) surface which serves as a model material for a cathode of solid oxide fuel cells. The dissociative adsorption of O(2) molecules from the gas phase is energetically favorable on surface Mn ions even on a defect-free surface. The surface migration energy for adsorbed O ions is found to be quite high, 2.0 eV. We predict that the adsorbed O atoms could penetrate the electrode first plane when much more mobile surface oxygen vacancies (migration energy of 0.69 eV) approach the O ions strongly bound to the surface Mn ions. The formation of the O vacancy near the O atom adsorbed atop surface Mn ion leads to an increase of the O-Mn binding energy by 0.74 eV whereas the drop of this adsorbed O atom into a vacancy possesses no energy barrier. Ab initio thermodynamics predicts that at typical SOFC operation temperatures (approximately 1200 K) the MnO(2) (001) surface with adsorbed O atoms is the most stable in a very wide range of oxygen gas pressures (above 10(-2) atm).     

Brownian dynamics simulations of polyelectrolyte adsorption onto charged patterned surfaces

The adsorption of single polyelectrolyte molecules onto surfaces decorated with periodic arrays of charged patches was studied using Brownian dynamics simulations. A free-draining, freely jointed bead-rod chain was used to model the polyelectrolyte, and electrostatic interactions were incorporated using a screened Coulombic potential with the excluded volume accounted for by a hard-sphere potential. The simulations predicted that the polyelectrolyte lies close to the adsorbing surface if the patch length, surface charge density, and screening length are sufficiently large. Chain conformations were found to be very sensitive to patch length, patch spacing, and the nature of the charge on adjacent patches. This is due both to the size of the polymer relative to patch length and spacing and to the structure of the electric field near the surface. In some cases, the component of the radius of gyration parallel to the surface can be made smaller than its free-solution value, which is contrary to what is observed for a uniformly charged surface. Isolated charged patches were also considered, and significant adsorption was observed above a critical surface charge density. The results demonstrate how polyelectrolyte conformations can be controlled by the design of the charged patches and may be useful for applications in which adsorbed polyelectrolyte films play a key role.     

Simulation Study on the Coil‐Globule Transition and Surface Adsorption of HP Chains

The coil‐globule transition of short hydrophobic‐polar (HP) chains, composed of 24 hydrophilic monomers and 24 polar monomers, in solution and on hydrophobic surface and the adsorption of the HP chain on hydrophobic surface are simulated. The coil‐globule transition point of the HP chain is dependent on sequence of chain but is roughly independent of the surface adsorption strength. Whereas the critical adsorption point of the HP chain is roughly independent of sequence. In addition, the lowest energy states can be obtained for the HP chain in solution or on surface by Monte Carlo simulated annealing method. Results show that the statistical conformation is strongly dependent on the intrachain H‐H attraction strength and the surface adsorption strength.